Technical Abstract:
Nearly 300 new microsatellite, or simple sequence repeat (SSR) markers were developed from genomic sequences of carrot. Efforts to map these markers and evaluate their usefulness in diversity studies are underway. In one F2 carrot population, a total of 51 polymorphic markers, including 37 codominant and 14 dominant SSRs, were placed in the reference carrot genetic map developed from a domesticated (B493) × wild (QAL) carrot cross. The mapped SSRs were distributed across all 9 linkage groups (LGs) of the carrot genome, with 3 to 9 markers/LG, recommending their usefulness for merging maps. Three SSRs in LG2 and LG5 were located in the vicinity of two highly-significant quantitative trait loci (QTL) for root carotenoid accumulation. Several microsatellites were closely linked (<10cM) to 16 carotenoid biosynthesis structural genes, suggesting that these repeats are relatively frequent in genic regions of the carrot genome. Ten unlinked microsatellite loci were used to investigate genetic relationships among 77 cultivated and wild Daucus accessions from diverse origins. In this germplasm, 214 alleles were identified, with an average of 21.4 alleles/SSR (range was 10-30) and a mean heterozygosity of 0.84. Cluster analysis revealed a structured population, generally differentiating wild carrot from cultivated carrots. When other wild Daucus subspecies and species were included in the analysis, they were usually clustered with the wild carrot accessions. A relatively high degree of marker transferability to carrot-related taxa suggests their potential applicability in other Apiaceae.